tbuckley/cabot-search huggingface dataset:
Regulation of epithelial transitional states in murine and human pulmonary fibrosis
Authors: Fa Wang, Christopher Ting, Kent A. Riemondy, Michael Douglas, Kendall Foster, Nisha Patel, Norihito Kaku, Alexander Linsalata, Jean Nemzek, Brian M. Varisco, Erez Cohen, Jasmine A. Wilson, David W.H. Riches, Elizabeth F. Redente, Diana M. Toivola, Xiaofeng Zhou, Bethany B. Moore, Pierre A. Coulombe, M. Bishr Omary, Rachel L. Zemans
Journal: Journal of Clinical Investigation (2023)

Idiopathic Pulmonary Fibrosis (IPF) is a progressive scarring disease arising from impaired regeneration of the alveolar epithelium after injury. During regeneration, type 2 alveolar epithelial cells (AEC2s) assume a transitional state that upregulates multiple keratins, and ultimately differentiate into AEC1s. In IPF, transitional AECs accumulate with ineffectual AEC1 differentiation. However, whether and how transitional cells cause fibrosis, whether keratins regulate transitional cell accumulation and fibrosis, and why transitional AECs and fibrosis resolve in mouse models but accumulate in IPF are unclear. Here, we show that human keratin (KRT) 8 genetic variants are associated with IPF. Krt8-/- mice are protected from fibrosis and accumulation of the transitional state. Keratin (K) 8 regulates expression of macrophage chemokines and macrophage recruitment. Profibrotic macrophages and myofibroblasts promote accumulation of transitional AECs, establishing a K8-dependent positive feedback loop driving fibrogenesis. Finally, rare murine transitional AECs are highly senescent, basaloid, and do not differentiate into AEC1s, recapitulating the aberrant basaloid state in human IPF. We conclude that transitional AECs induce and are maintained by fibrosis in a K8-dependent manner; in mice, most transitional cells and fibrosis resolve, whereas in human IPF, transitional AECs evolve into an aberrant basaloid state which persists with progressive fibrosis.
Incomplete language-of-thought in infancy
Authors: Jean-Rémy Hochmann
Journal: Behavioral and Brain Sciences (2023)

Abstract The view that infants possess a full-fledged propositional language-of-thought (LoT) is appealing, providing a unifying account for infants’ precocious reasoning skills in many domains. However, careful appraisal of empirical evidence suggests that there is still no convincing evidence that infants possess discrete representations of abstract relations, suggesting that infants’ LoT remains incomplete. Parallel arguments hold for perception.
Uncovering Rare Coding Variants in IgA Nephropathy
Authors: Jian Liu, Jingyuan Xie
Journal: Journal of the American Society of Nephrology (2023)

1Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China 2Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, Shanghai, China Correspondence: Dr. Jingyuan Xie, Department of Nephrology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Institute of Nephrology, Shanghai Jiao Tong University School of Medicine, No. 197 Ruijin Er Road, Huangpu District, Shanghai, 200025, China. Email: [email protected] Published online ahead of print. Publication date available at www.jasn.org. See related article, "Genome-Wide Association Analysis of Protein-Coding Variants in IgA Nephropathy," on pages 1900–1913.
Household laundry detergents disrupt barrier integrity and induce inflammation in mouse and human skin
Authors: Arturo O. Rinaldi, Manru Li, Elena Barletta, Paolo D'Avino, Duygu Yazici, Yagiz Pat, Siobhan Ward, Daniel Burla, Ge Tan, Nima Askary, Rasmus Larsson, Jeremy Bost, Huseyn Babayev, Raja Dhir, Nicolas Gaudenzio, Mubeccel Akdis, Kari Nadeau, Cezmi A. Akdis, Yasutaka Mitamura
Journal: Allergy (2023)

Abstract Background Epithelial barrier impairment is associated with many skin and mucosal inflammatory disorders. Laundry detergents have been demonstrated to affect epithelial barrier function in vitro using air–liquid interface cultures of human epithelial cells. Methods Back skin of C57BL/6 mice was treated with two household laundry detergents at several dilutions. Barrier function was assessed by electric impedance spectroscopy (EIS) and transepidermal water loss (TEWL) measurements after the 4 h of treatments with detergents. RNA sequencing (RNA‐seq) and targeted multiplex proteomics analyses in skin biopsy samples were performed. The 6‐h treatment effect of laundry detergent and sodium dodecyl sulfate (SDS) was investigated on ex vivo human skin. Results Detergent‐treated skin showed a significant EIS reduction and TEWL increase compared to untreated skin, with a relatively higher sensitivity and dose–response in EIS. The RNA‐seq showed the reduction of the expression of several genes essential for skin barrier integrity, such as tight junctions and adherens junction proteins. In contrast, keratinization, lipid metabolic processes, and epidermal cell differentiation were upregulated. Proteomics analysis showed that the detergents treatment generally downregulated cell adhesion‐related proteins, such as epithelial cell adhesion molecule and contactin‐1, and upregulated proinflammatory proteins, such as interleukin 6 and interleukin 1 beta. Both detergent and SDS led to a significant decrease in EIS values in the ex vivo human skin model. Conclusion The present study demonstrated that laundry detergents and its main component, SDS impaired the epidermal barrier in vivo and ex vivo human skin. Daily detergent exposure may cause skin barrier disruption and may contribute to the development of atopic diseases.
Assessing the genetic risk of nodular melanoma using a candidate gene approach
Authors: Mitchell S Stark, Richard A Sturm, Yan Pan, Darren J Smit, Varsha Kommajosyula, Katie J Lee, Kasturee Jagirdar, Catriona McLean, David L Duffy, H Peter Soyer, Victoria J Mar
Journal: British Journal of Dermatology (2023)

Nodular melanoma (NM) is a challenge to diagnose early due to its rapid growth and more atypical clinical presentation, making it the largest contributor to melanoma mortality.
Genomic Variation, Population History, and Long-Term Genetic Adaptation to High Altitudes in Tibetan Partridge (<i>Perdix hodgsoniae</i>)
Authors: Catalina Palacios, Pengcheng Wang, Nan Wang, Megan A Brown, Lukas Capatosto, Juan Du, Jiahu Jiang, Qingze Zhang, Nishma Dahal, Sangeet Lamichhaney
Journal: Molecular Biology and Evolution (2023)

Species residing across elevational gradients display adaptations in response to environmental changes such as oxygen availability, ultraviolet radiation, and temperature. Here, we study genomic variation, gene expression, and long-term adaptation in Tibetan Partridge (Perdix hodgsoniae) populations residing across the elevational gradient of the Tibetan Plateau. We generated a high-quality draft genome and used it to carry out downstream population genomic and transcriptomic analysis. The P. hodgsoniae populations residing across various elevations were genetically distinct, and their phylogenetic clustering was consistent with their geographic distribution. We identified possible evidence of gene flow between populations residing in <3,000 and >4,200 m elevation that is consistent with known habitat expansion of high-altitude populations of P. hodgsoniae to a lower elevation. We identified a 60 kb haplotype encompassing the Estrogen Receptor 1 (ESR1) gene, showing strong genetic divergence between populations of P. hodgsoniae. We identified six single nucleotide polymorphisms within the ESR1 gene fixed for derived alleles in high-altitude populations that are strongly conserved across vertebrates. We also compared blood transcriptome profiles and identified differentially expressed genes (such as GAPDH, LDHA, and ALDOC) that correlated with differences in altitude among populations of P. hodgsoniae. These candidate genes from population genomics and transcriptomics analysis were enriched for neutrophil degranulation and glycolysis pathways, which are known to respond to hypoxia and hence may contribute to long-term adaptation to high altitudes in P. hodgsoniae. Our results highlight Tibetan Partridges as a useful model to study molecular mechanisms underlying long-term adaptation to high altitudes.
Do nonlinguistic creatures deploy mental symbols for logical connectives in reasoning?
Authors: Susan Carey
Journal: Behavioral and Brain Sciences (2023)

Abstract Some nonlinguistic systems of representation display some of the six features of a language-of-thought (LoT) delineated by Quilty-Dunn et al. But they conjecture something stronger: That all six features cooccur homeostatically in nonlinguistic thought. Here I argue that there is no good evidence for nonlinguistic deductive reasoning involving the disjunctive syllogism. Animals and prelinguistic children probably do not make logical inferences.
Reattribution to Mind-Brain Processes and Recovery From Chronic Back Pain
Authors: Yoni K. Ashar, Mark A. Lumley, Roy H. Perlis, Conor Liston, Faith M. Gunning, Tor D. Wager
Journal: JAMA Network Open (2023)

In primary chronic back pain (CBP), the belief that pain indicates tissue damage is both inaccurate and unhelpful. Reattributing pain to mind or brain processes may support recovery.
A language of episodic thought?
Authors: Johannes B. Mahr, Daniel L. Schacter
Journal: Behavioral and Brain Sciences (2023)

We propose that episodic thought (i.e., episodic memory and imagination) is a domain where the language-of-thought hypothesis (LoTH) could be fruitfully applied. On the one hand, LoTH could explain the structure of what is encoded into and retrieved from long-term memory. On the other, LoTH can help make sense of how episodic contents come to play such a large variety of different cognitive roles after they have been retrieved.
Increased reports of severe myocarditis associated with enterovirus infection in neonates, United Kingdom, 27 June 2022 to 26 April 2023
Authors: Anika Singanayagam, Catherine Moore, Susannah Froude, Cristina Celma, Julia Stowe, Erjola Hani, Khuen Foong Ng, Peter Muir, Marion Roderick, Simon Cottrell, David F. Bibby, Barry Vipond, Sophie Gillett, Peter J. Davis, Jack Gibb, Mai Barry, Phillippa Harris, Frances Rowley, Jiao Song, Ananda Giri Shankar, Danielle McMichael, Jonathan M. Cohen, Abirami Manian, Ciaran Harvey, Louise Shaw Primrose, Stefanie Wilson, Declan T. Bradley, Karthik Paranthaman, Stuart Beard, Maria Zambon, Mary Ramsay, Vanessa Saliba, Shamez Ladhani, Christopher Williams
Journal: Eurosurveillance (2023)

Enteroviruses are a common cause of seasonal childhood infections. The vast majority of enterovirus infections are mild and self-limiting, although neonates can sometimes develop severe disease. Myocarditis is a rare complication of enterovirus infection. Between June 2022 and April 2023, twenty cases of severe neonatal enteroviral myocarditis caused by coxsackie B viruses were reported in the United Kingdom. Sixteen required critical care support and two died. Enterovirus PCR on whole blood was the most sensitive diagnostic test. We describe the initial public health investigation into this cluster and aim to raise awareness among paediatricians, laboratories and public health specialists.
Language-of-thought hypothesis: Wrong, but sometimes useful?
Authors: Adina L. Roskies, Colin Allen
Journal: Behavioral and Brain Sciences (2023)

Abstract Quilty-Dunn et al. maintain that language-of-thought hypothesis (LoTH) is the best game in town. We counter that LoTH is merely one source of models – always wrong, sometimes useful. Their reasons for liking LoTH are compatible with the view that LoTH provides a sometimes pragmatically useful level of abstraction over processes and mechanisms that fail to fully live up to LoT requirements.
Costs for Long-Term Health Care After a Police Shooting in Ontario, Canada
Authors: Sheharyar Raza, Deva Thiruchelvam, Donald A. Redelmeier
Journal: JAMA Network Open (2023)

Police shootings can cause serious acute injury, and knowledge of subsequent health outcomes may inform interventions to improve care.To analyze long-term health care costs among survivors of police shootings compared with those surviving nonfirearm police enforcement injuries using a retrospective design.This population-based cohort analysis identified adults (age ≥16 years) who were injured by police and required emergency medical care between April 1, 2002, and March 31, 2022, in Ontario, Canada.Police shootings compared with other mechanisms of injury involving police.Long-term health care costs determined using a validated costing algorithm. Secondary outcomes included short-term mortality, acute care treatments, and rates of subsequent disability.Over the study, 13 545 adults were injured from police enforcement (mean [SD] age, 35 [12] years; 11 637 males [86%]). A total of 13 520 individuals survived acute injury, and 8755 had long-term financial data available (88 surviving firearm injury, 8667 surviving nonfirearm injury). Patients surviving firearm injury had 3 times greater health care costs per year (CAD$16 223 vs CAD$5412; mean increase, CAD$9967; 95% CI, 6697-13 237; US $11 982 vs US $3997; mean increase, US $7361; 95% CI, 4946-9776; P < .001). Greater costs after a firearm injury were not explained by baseline costs and primarily reflected increased psychiatric care. Other characteristics associated with increased long-term health care costs included prior mental illness and a substance use diagnosis.In this longitudinal cohort study of long-term health care costs, patients surviving a police shooting had substantial health care costs compared with those injured from other forms of police enforcement. Costs primarily reflected psychiatric care and suggest the need to prioritize early recognition and prevention.
Linguistic structure and the languages-of-thought
Authors: Gabe Dupre
Journal: Behavioral and Brain Sciences (2023)

Abstract Quilty-Dunn et al. adopt a methodology for psychology connecting behavioral capacities to the format of the mental systems underlying them. This methodology opens up avenues connecting linguistic theory to comparative psychology. On the assumption that language structures thought, identifying the formal structure of human language can generate hypotheses connecting distinctively human cognitive traits to the distinctive structures of human language.
Supra and subgingival application of antiseptics or antibiotics during periodontal therapy
Authors: Elena Figuero, Jorge Serrano, Nicole Birgit Arweiler, Thorsten Mathias Auschill, Ali Gürkan, Gülnur Emingil
Journal: Periodontology 2000 (2023)

Abstract Periodontal diseases (gingivitis and periodontitis) are characterized by inflammatory processes which arise as a result of disruption of the balance in the oral ecosystem. According to the current S3 level clinical practice guidelines, therapy of patients with periodontitis involves a stepwise approach that includes the control of the patient's risk factors and the debridement of supra and subgingival biofilm. This debridement can be performed with or without the use of some adjuvant therapies, including physical or chemical agents, host modulating agents, subgingivally locally delivered antimicrobials, or systemic antimicrobials. Therefore, the main aim of this article is to review in a narrative manner the existing literature regarding the adjuvant application of local agents, either subgingivally delivered antibiotics and antiseptics or supragingivally applied rinses and dentifrices, during the different steps in periodontal therapy performed in Europe.
The computational and the representational language-of-thought hypotheses
Authors: David J. Chalmers
Journal: Behavioral and Brain Sciences (2023)

Abstract There are two versions of the language-of-thought hypothesis (LOT): Representational LOT (roughly, structured representation), introduced by Ockham, and computational LOT (roughly, symbolic computation) introduced by Fodor. Like many others, I oppose the latter but not the former. Quilty-Dunn et al. defend representational LOT, but they do not defend the strong computational LOT thesis central to the classical-connectionist debate.
Ending One’s Life Is Not Always a Sign of Psychopathology—Reply
Authors: Alexandra L. Potter, Chinmay Haridas, Chi-Fu Jeffrey Yang
Journal: JAMA Oncology (2023)

Our website uses cookies to enhance your experience. By continuing to use our site, or clicking "Continue," you are agreeing to our Cookie Policy | Continue JAMA Oncology HomeNew OnlineCurrent IssueFor Authors Podcast Journals JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry (1919-1959) JN Learning / CMESubscribeJobsInstitutions / LibrariansReprints & Permissions Terms of Use | Privacy Policy | Accessibility Statement 2024 American Medical Association. All Rights Reserved Search All JAMA JAMA Network Open JAMA Cardiology JAMA Dermatology JAMA Forum Archive JAMA Health Forum JAMA Internal Medicine JAMA Neurology JAMA Oncology JAMA Ophthalmology JAMA Otolaryngology–Head & Neck Surgery JAMA Pediatrics JAMA Psychiatry JAMA Surgery Archives of Neurology & Psychiatry Input Search Term Sign In Individual Sign In Sign inCreate an Account Access through your institution Sign In Purchase Options: Buy this article Rent this article Subscribe to the JAMA Oncology journal
On the hazards of relating representations and inductive biases
Authors: Thomas L. Griffiths, Sreejan Kumar, R. Thomas McCoy
Journal: Behavioral and Brain Sciences (2023)

Abstract The success of models of human behavior based on Bayesian inference over logical formulas or programs is taken as evidence that people employ a “language-of-thought” that has similarly discrete and compositional structure. We argue that this conclusion problematically crosses levels of analysis, identifying representations at the algorithmic level based on inductive biases at the computational level.
Compositionality in visual perception
Authors: Alon Hafri, E. J. Green, Chaz Firestone
Journal: Behavioral and Brain Sciences (2023)

Quilty-Dunn et al.'s wide-ranging defense of the Language of Thought Hypothesis (LoTH) argues that vision traffics in abstract, structured representational formats. We agree: Vision, like language, is compositional - just as words compose into phrases, many visual representations contain discrete constituents that combine in systematic ways. Here, we amass evidence extending this proposal, and explore its implications for how vision interfaces with the rest of the mind.
Radiotherapy Plus Cisplatin With or Without Lapatinib for Non–Human Papillomavirus Head and Neck Carcinoma
Authors: Stuart J. Wong, Pedro A. Torres-Saavedra, Nabil F. Saba, George Shenouda, Jeffrey M. Bumpous, Robert E. Wallace, Christine H. Chung, Adel K. El-Naggar, Clement K. Gwede, Barbara Burtness, Paul A. Tennant, Neal E. Dunlap, Rebecca Redman, William A. Stokes, Soumon Rudra, Loren K. Mell, Assuntina G. Sacco, Sharon A. Spencer, Lisle Nabell, Min Yao, Fabio L. Cury, Darrion L. Mitchell, Christopher U. Jones, Selim Firat, Joseph N. Contessa, Thomas Galloway, Adam Currey, Jonathan Harris, Walter J. Curran, Quynh-Thu Le
Journal: JAMA Oncology (2023)

Patients with locally advanced non-human papillomavirus (HPV) head and neck cancer (HNC) carry an unfavorable prognosis. Chemoradiotherapy (CRT) with cisplatin or anti-epidermal growth factor receptor (EGFR) antibody improves overall survival (OS) of patients with stage III to IV HNC, and preclinical data suggest that a small-molecule tyrosine kinase inhibitor dual EGFR and ERBB2 (formerly HER2 or HER2/neu) inhibitor may be more effective than anti-EGFR antibody therapy in HNC.
The reemergence of the language-of-thought hypothesis: Consequences for the development of the logic of thought
Authors: Nicolò Cesana-Arlotti
Journal: Behavioral and Brain Sciences (2023)

Abstract Quilty-Dunn et al. defended the reemergence of language-of-thought hypothesis (LoTH). My commentary builds up implications for the study of the development of our logical capacities. Empirical support for logically augmented LoT systems calls for the investigation of their logical primitives and developmental origin. Furthermore, Quilty-Dunn et al.'s characterization of LoT helps the quest for the foundation of logic by dissociating logical cognition from natural language.
Exposure to Neighborhood Walkability and Residential Greenness and Incident Fracture
Authors: Zhanghang Zhu, Zongming Yang, Lisha Xu, Yonghao Wu, Luhua Yu, Peng Shen, Hongbo Lin, Liming Shui, Mengling Tang, Mingjuan Jin, Jianbing Wang, Kun Chen
Journal: JAMA Network Open (2023)

Emerging studies have suggested that environmental factors are associated with fracture. However, little is known about the association of neighborhood walkability and residential greenness with fracture.To investigate the association of long-term exposure to walkability and greenness with incident fracture and explore the potential interaction effect.This cohort study recruited participants aged 40 years or older in Ningbo, China from June 2015 to January 2018. Participants were observed for outcomes through February 2023, with data analysis conducted in March 2023.Neighborhood walkability was measured by a modified walkability calculation method according to a walk score tool. Residential greenness was assessed by satellite-derived normalized difference vegetation index (NDVI) within a 1000-m buffer.Incident fracture was ascertained according to International Statistical Classification of Diseases and Related Health Problems, Tenth Revision codes via the Yinzhou Health Information System. Cox proportional hazards models were fit, with age as time scale to estimate the associations of walkability and greenness with fracture. Potential effect modification was explored by covariates, as well as the interactive effect of walkability and greenness.A total of 23 940 participants were included in this study with 13 735 being female (57.4%). The mean (SD) age at baseline was 63.4 (9.4) years. During a follow-up period of 134 638 person-years, 3322 incident fractures were documented. In the full adjusted model, every IQR increment in neighborhood walkability and residential greenness was associated with a hazard ratio (HR) of 0.88 (95% CI, 0.83-0.92) and 0.84 (95% CI, 0.80-0.89), respectively, for fracture. Furthermore, the association of greenness and fracture was greater with an increase in walkability. The HR (Q4 vs Q1) for greenness was 0.62 (95% CI, 0.46-0.82) in neighborhoods with the highest quartile of walkability.This population cohort study suggested that long-term exposure to neighborhood walkability and residential greenness were both associated with lower risk of incident fracture. The benefits of greenness increased in more walkable areas.
Safety, Tolerability, Pharmacokinetics, and Preliminary Efficacy of YK-029A in Treatment-Naive Patients With Advanced NSCLC Harboring EGFR Exon 20 Insertion Mutations: A Phase 1 Trial
Authors: Jianchun Duan, Lin Wu, Kunyu Yang, Jun Zhao, Yanqiu Zhao, Xiumei Dai, Mingjun Li, Yanyan Xie, Yu Yao, Mingfang Zhao, Chengzhi Zhou, Xiubao Ren, Zhe Liu, Yueyin Pan, Yuping Li, Baogang Liu, Ying Cheng, Liyun Miao, Qitao Yu, Zhihong Zhang, Xiaoqing Liu, Jiuwei Cui, Yu Zhang, Li Zhang, Xiaoyan Li, Xiaoling Li, Bo Shen, Bi Chen, Shan Zeng, Bin Li, Yanping Hu, Lin Li, Rong Wu, Qibin Song, Jie Wang
Journal: Journal of Thoracic Oncology (2023)
Impact of time to surgical treatment in Merkel cell carcinoma: Surveillance, Epidemiology, and End Results–based population study
Authors: Stephanie K. Lin, Annika M. Deitermann, Dylan Haynes, Kaley Ricciardelli, Jeremy R. Etzkorn, Christopher J. Miller, H. William Higgins, Cerrene N. Giordano, Stacy L. McMurray, Joanna L. Walker, Junqian Zhang, Harrison P. Nguyen, Joseph F. Sobanko
Journal: Journal of the American Academy of Dermatology (2023)